These two models are similar enough that I'd fall in with those who suggest buying the best example of either that you can find/afford. This said, I had a couple of standard GS's, an 89 and a 91, and will offer what I can..
Very close to the same bike, the 90-94 bikes had the little fairing which I wound up liking.. there's a built-in tach, and a small dash that allows for cleaner installation of switchgear if you have heated grips or the like. These bikes had marginally better brakes, with a drilled floating front disc, though none of the airhead GS family are famous for stopping power.
Similarly, the later bikes had an adjustable rear shock, but most with the money would go for a suspension upgrade anyway. This is the bike they call the gummy cow, after all..
I always thought the PD looked cool, and probably would have bought one given the right opportunity. My local BMW wrench/dealer at the time said that the PD's tended to run hotter due to the large tank and high fender, (less flow reaching the block) and were hard on chassis electrics, particularly diode boards. He also felt that they were more prone to the driveshaft failure that bothers all of these bikes, but have not heard that substantiated elsewhere.
And I wouldn't call any of these bikes pretty, except in a swiss-army-kinife sort of way. They came in some pretty outlandish color schemes, particularly the PD. See if you can find the pink-white-teal combo with the treadmarks on the tank.